Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= TCDB::Q8GBT6 (403 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 236 bits (601), Expect = 1e-66 Identities = 137/391 (35%), Positives = 216/391 (55%), Gaps = 23/391 (5%) Query: 5 QRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAG-FMAAGGNAILDNMALL 63 QR+ ++L++P+A+LPAA +++ + + F+ +A M + G I D M +L Sbjct: 24 QRLSQTLLIPIAILPAAGVMIGIATNPL-------PFIPDVANVLMLSVGKLIFDIMPML 76 Query: 64 FAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATFTDK-NLPQVAKAVDGKVVMVDAPVD 122 FA+ +AIGF + G A +A GY V + LA +LP +V +D Sbjct: 77 FAIAVAIGFCR-DQGIAAFSAAFGYGVLLSTLAAAAKVYHLPS-------HIVWGTPTID 128 Query: 123 AKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPVL 182 + GG+++G + + + + +LP FF GRR P++ +++ ++ +IWP L Sbjct: 129 TGIAGGMLVGGITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPL 188 Query: 183 GTGLHNFGEWLV-GSGAVGAGIFGVANRALIPIGMHHLLNSFPWFQAGEY----EGKSGD 237 + +W V A+ G +G+ R L+P+G+HH+ N+ + + G+Y E G+ Sbjct: 189 ALSIERLSDWAVYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHDGEIVRGE 248 Query: 238 IARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFVTG 297 +AR+ AGDP+AG G+ I M+ LPAA LAI CA +R V G+M S A S++TG Sbjct: 249 MARYFAGDPSAGNLAGGYL-IKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTG 307 Query: 298 VTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASNPW 357 VTEPIEF F+F+AP+LY HA+LTG++ ++ L M FS G VDF L +SN Sbjct: 308 VTEPIEFAFLFVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTH 367 Query: 358 GLALVGVCFAALYYVVFRFAITKFNLPTPGR 388 + +G +YY++FR +I FNL TPGR Sbjct: 368 WIWFLGPLTFVIYYILFRASILAFNLKTPGR 398 Lambda K H 0.328 0.143 0.441 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 526 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 403 Length of database: 485 Length adjustment: 32 Effective length of query: 371 Effective length of database: 453 Effective search space: 168063 Effective search space used: 168063 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory